The US Navy has cancelled visits to the Philippine port of Subic amid public anger over accusations that a US Marine killed a Filipino on the city's outskirts, officials said Monday.

Foreign Department spokesman Charles Jose said the visits of three US ships to Subic this month had been cancelled, while the head of the Subic freeport said nine such visits scheduled for this year had been called off.

"The DFA (Department of Foreign Affairs) was informed through normal diplomatic channels of the cancellation of the visits to Subic of three ships for operational reasons," he said.

Jose told reporters he did not believe the cancellations were linked to anger stirred by the investigation of a US Marine for the killing of a Filipina in Olongapo City last month.

Subic Bay Metropolitan Authority chairman Robert Garcia said nine US ships due to dock at Subic this year had cancelled their visits.

He told AFP that two US Navy ships were still scheduled to make port calls in Subic for "emergency repairs" but their crews would not be allowed to disembark.

Normally, two or three US Navy ships make routine port calls every month for resupply in Subic, a former US naval base about an hour's drive from Manila, said Garcia.

He said the authority had been informed of the cancellations by the Subic chamber of commerce, which includes the company that services US ships.

However Garcia could not say why the visits were cancelled. US embassy officials declined to comment.

Jennifer Laude, a 26-year-old transgender Filipina, was found dead on October 12 in a cheap hotel near Subic with marks of strangulation on her neck.

US Marine Private First Class Joseph Scott Pemberton, who had just finished taking part in US-Philippine military exercises in Subic, had checked into the hotel with Laude and was the last person seen with her, police said.

Pemberton is now detained at Philippine military headquarters while prosecutors consider charging him.

Activist groups have seized on the incident to attack the defence ties between the United States and its former colony.

Frequent street protests have been staged against the US forces.